Starting phenix.real_space_refine on Fri May 16 20:14:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dpt_27642/05_2025/8dpt_27642.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dpt_27642/05_2025/8dpt_27642.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dpt_27642/05_2025/8dpt_27642.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dpt_27642/05_2025/8dpt_27642.map" model { file = "/net/cci-nas-00/data/ceres_data/8dpt_27642/05_2025/8dpt_27642.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dpt_27642/05_2025/8dpt_27642.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1420 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 46 5.16 5 C 8608 2.51 5 N 2330 2.21 5 O 2566 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 13550 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3169 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 375} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TRP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 1262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1262 Classifications: {'peptide': 165} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 150} Chain: "C" Number of atoms: 2249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2249 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 33, 'TRANS': 260} Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Restraints were copied for chains: F, H, D, E, L Time building chain proxies: 9.94, per 1000 atoms: 0.73 Number of scatterers: 13550 At special positions: 0 Unit cell: (148.03, 184.71, 137.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 46 16.00 O 2566 8.00 N 2330 7.00 C 8608 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 6 " - pdb=" SG CYS A 32 " distance=2.03 Simple disulfide: pdb=" SG CYS A 26 " - pdb=" SG CYS A 81 " distance=2.03 Simple disulfide: pdb=" SG CYS A 112 " - pdb=" SG CYS A 122 " distance=2.03 Simple disulfide: pdb=" SG CYS A 150 " - pdb=" SG CYS A 160 " distance=2.03 Simple disulfide: pdb=" SG CYS C 4 " - pdb=" SG CYS C 25 " distance=2.03 Simple disulfide: pdb=" SG CYS C 26 " - pdb=" SG CYS C 72 " distance=2.03 Simple disulfide: pdb=" SG CYS C 98 " - pdb=" SG CYS C 108 " distance=2.03 Simple disulfide: pdb=" SG CYS C 148 " - pdb=" SG CYS C 158 " distance=2.03 Simple disulfide: pdb=" SG CYS D 6 " - pdb=" SG CYS D 32 " distance=2.03 Simple disulfide: pdb=" SG CYS D 26 " - pdb=" SG CYS D 81 " distance=2.03 Simple disulfide: pdb=" SG CYS D 112 " - pdb=" SG CYS D 122 " distance=2.03 Simple disulfide: pdb=" SG CYS D 150 " - pdb=" SG CYS D 160 " distance=2.03 Simple disulfide: pdb=" SG CYS F 4 " - pdb=" SG CYS F 25 " distance=2.03 Simple disulfide: pdb=" SG CYS F 26 " - pdb=" SG CYS F 72 " distance=2.03 Simple disulfide: pdb=" SG CYS F 98 " - pdb=" SG CYS F 108 " distance=2.03 Simple disulfide: pdb=" SG CYS F 148 " - pdb=" SG CYS F 158 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " NAG-ASN " NAG A 601 " - " ASN A 21 " " NAG A 602 " - " ASN A 135 " " NAG D 601 " - " ASN D 21 " " NAG D 602 " - " ASN D 135 " " NAG G 1 " - " ASN A 61 " " NAG H 1 " - " ASN D 61 " " NAG I 1 " - " ASN C 172 " " NAG L 1 " - " ASN F 172 " Time building additional restraints: 3.52 Conformation dependent library (CDL) restraints added in 1.9 seconds 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3212 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 34 sheets defined 19.5% alpha, 31.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.81 Creating SS restraints... Processing helix chain 'A' and resid 29 through 37 Processing helix chain 'A' and resid 39 through 41 No H-bonds generated for 'chain 'A' and resid 39 through 41' Processing helix chain 'A' and resid 53 through 55 No H-bonds generated for 'chain 'A' and resid 53 through 55' Processing helix chain 'A' and resid 193 through 196 Processing helix chain 'A' and resid 225 through 230 Processing helix chain 'A' and resid 251 through 256 removed outlier: 3.712A pdb=" N ALA A 256 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 338 Processing helix chain 'B' and resid 15 through 43 Processing helix chain 'B' and resid 68 through 94 removed outlier: 3.539A pdb=" N VAL B 72 " --> pdb=" O GLN B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 102 removed outlier: 4.371A pdb=" N THR B 100 " --> pdb=" O SER B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 126 removed outlier: 3.577A pdb=" N ARG B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 176 removed outlier: 3.864A pdb=" N LEU B 162 " --> pdb=" O GLY B 158 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ASP B 165 " --> pdb=" O HIS B 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 67 Processing helix chain 'C' and resid 190 through 194 Processing helix chain 'D' and resid 29 through 37 Processing helix chain 'D' and resid 39 through 41 No H-bonds generated for 'chain 'D' and resid 39 through 41' Processing helix chain 'D' and resid 53 through 55 No H-bonds generated for 'chain 'D' and resid 53 through 55' Processing helix chain 'D' and resid 193 through 196 Processing helix chain 'D' and resid 225 through 230 Processing helix chain 'D' and resid 251 through 256 removed outlier: 3.712A pdb=" N ALA D 256 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 338 Processing helix chain 'E' and resid 15 through 43 Processing helix chain 'E' and resid 68 through 94 removed outlier: 3.538A pdb=" N VAL E 72 " --> pdb=" O GLN E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 102 removed outlier: 4.371A pdb=" N THR E 100 " --> pdb=" O SER E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 126 removed outlier: 3.577A pdb=" N ARG E 114 " --> pdb=" O ALA E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 176 removed outlier: 3.864A pdb=" N LEU E 162 " --> pdb=" O GLY E 158 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ASP E 165 " --> pdb=" O HIS E 161 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 67 Processing helix chain 'F' and resid 190 through 194 Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 10 removed outlier: 6.622A pdb=" N ALA A 64 " --> pdb=" O ILE A 60 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 17 Processing sheet with id=AA3, first strand: chain 'A' and resid 50 through 51 removed outlier: 3.626A pdb=" N LYS A 46 " --> pdb=" O THR A 80 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE A 83 " --> pdb=" O ASN A 92 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N ASN A 92 " --> pdb=" O ILE A 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 159 through 161 removed outlier: 4.437A pdb=" N ASP A 125 " --> pdb=" O ASN A 109 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N ASN A 109 " --> pdb=" O ASP A 125 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N LYS A 199 " --> pdb=" O CYS A 112 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL A 114 " --> pdb=" O LYS A 199 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 145 through 146 removed outlier: 3.765A pdb=" N GLU A 173 " --> pdb=" O GLU A 141 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 150 through 151 removed outlier: 3.765A pdb=" N GLU A 173 " --> pdb=" O GLU A 141 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE A 192 " --> pdb=" O ILE A 172 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 204 through 209 removed outlier: 5.514A pdb=" N ASN A 205 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N THR A 223 " --> pdb=" O ASN A 205 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 248 through 249 removed outlier: 3.680A pdb=" N ARG A 278 " --> pdb=" O ASN A 236 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN A 238 " --> pdb=" O ARG A 276 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ARG A 276 " --> pdb=" O GLN A 238 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ARG A 240 " --> pdb=" O VAL A 274 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL A 274 " --> pdb=" O ARG A 240 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 310 through 316 removed outlier: 3.664A pdb=" N VAL A 325 " --> pdb=" O VAL A 367 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL A 367 " --> pdb=" O VAL A 325 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU A 327 " --> pdb=" O LEU A 365 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 356 through 360 removed outlier: 3.822A pdb=" N ASP A 343 " --> pdb=" O ARG A 381 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ALA A 376 " --> pdb=" O LEU A 392 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU A 392 " --> pdb=" O ALA A 376 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU A 378 " --> pdb=" O ALA A 390 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 14 through 16 removed outlier: 3.761A pdb=" N GLN C 14 " --> pdb=" O THR C 84 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLN C 86 " --> pdb=" O GLN C 14 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N LEU C 79 " --> pdb=" O THR C 74 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N THR C 74 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY C 81 " --> pdb=" O CYS C 72 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 22 through 25 Processing sheet with id=AB4, first strand: chain 'C' and resid 95 through 99 removed outlier: 3.798A pdb=" N CYS C 108 " --> pdb=" O CYS C 158 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 121 through 128 removed outlier: 3.625A pdb=" N ARG C 121 " --> pdb=" O VAL C 176 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 121 through 128 removed outlier: 3.625A pdb=" N ARG C 121 " --> pdb=" O VAL C 176 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 200 through 206 removed outlier: 6.305A pdb=" N GLY C 201 " --> pdb=" O THR C 219 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N THR C 219 " --> pdb=" O GLY C 201 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 247 through 249 Processing sheet with id=AB9, first strand: chain 'D' and resid 8 through 10 removed outlier: 6.623A pdb=" N ALA D 64 " --> pdb=" O ILE D 60 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 15 through 17 Processing sheet with id=AC2, first strand: chain 'D' and resid 50 through 51 removed outlier: 3.627A pdb=" N LYS D 46 " --> pdb=" O THR D 80 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE D 83 " --> pdb=" O ASN D 92 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N ASN D 92 " --> pdb=" O ILE D 83 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 159 through 161 removed outlier: 4.437A pdb=" N ASP D 125 " --> pdb=" O ASN D 109 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N ASN D 109 " --> pdb=" O ASP D 125 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N LYS D 199 " --> pdb=" O CYS D 112 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL D 114 " --> pdb=" O LYS D 199 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 145 through 146 removed outlier: 3.765A pdb=" N GLU D 173 " --> pdb=" O GLU D 141 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 150 through 151 removed outlier: 3.765A pdb=" N GLU D 173 " --> pdb=" O GLU D 141 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE D 192 " --> pdb=" O ILE D 172 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 204 through 209 removed outlier: 5.514A pdb=" N ASN D 205 " --> pdb=" O THR D 223 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N THR D 223 " --> pdb=" O ASN D 205 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 248 through 249 removed outlier: 3.679A pdb=" N ARG D 278 " --> pdb=" O ASN D 236 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN D 238 " --> pdb=" O ARG D 276 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG D 276 " --> pdb=" O GLN D 238 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ARG D 240 " --> pdb=" O VAL D 274 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL D 274 " --> pdb=" O ARG D 240 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 310 through 316 removed outlier: 3.664A pdb=" N VAL D 325 " --> pdb=" O VAL D 367 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL D 367 " --> pdb=" O VAL D 325 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU D 327 " --> pdb=" O LEU D 365 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 356 through 360 removed outlier: 3.822A pdb=" N ASP D 343 " --> pdb=" O ARG D 381 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ALA D 376 " --> pdb=" O LEU D 392 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU D 392 " --> pdb=" O ALA D 376 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU D 378 " --> pdb=" O ALA D 390 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 14 through 16 removed outlier: 3.760A pdb=" N GLN F 14 " --> pdb=" O THR F 84 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLN F 86 " --> pdb=" O GLN F 14 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LEU F 79 " --> pdb=" O THR F 74 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N THR F 74 " --> pdb=" O LEU F 79 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY F 81 " --> pdb=" O CYS F 72 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 22 through 25 Processing sheet with id=AD3, first strand: chain 'F' and resid 95 through 99 removed outlier: 3.797A pdb=" N CYS F 108 " --> pdb=" O CYS F 158 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 121 through 128 removed outlier: 3.624A pdb=" N ARG F 121 " --> pdb=" O VAL F 176 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 121 through 128 removed outlier: 3.624A pdb=" N ARG F 121 " --> pdb=" O VAL F 176 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 200 through 206 removed outlier: 6.305A pdb=" N GLY F 201 " --> pdb=" O THR F 219 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N THR F 219 " --> pdb=" O GLY F 201 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 247 through 249 548 hydrogen bonds defined for protein. 1410 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.34 Time building geometry restraints manager: 4.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 4370 1.35 - 1.47: 3344 1.47 - 1.59: 6148 1.59 - 1.71: 0 1.71 - 1.83: 56 Bond restraints: 13918 Sorted by residual: bond pdb=" C1 NAG I 1 " pdb=" O5 NAG I 1 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.33e+00 bond pdb=" C1 NAG L 1 " pdb=" O5 NAG L 1 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.27e+00 bond pdb=" CA ASP F 151 " pdb=" C ASP F 151 " ideal model delta sigma weight residual 1.524 1.548 -0.024 1.26e-02 6.30e+03 3.67e+00 bond pdb=" CA ASP C 151 " pdb=" C ASP C 151 " ideal model delta sigma weight residual 1.524 1.546 -0.023 1.26e-02 6.30e+03 3.20e+00 bond pdb=" C1 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.92e+00 ... (remaining 13913 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.90: 18721 3.90 - 7.80: 279 7.80 - 11.70: 30 11.70 - 15.60: 6 15.60 - 19.50: 4 Bond angle restraints: 19040 Sorted by residual: angle pdb=" CG ARG B 85 " pdb=" CD ARG B 85 " pdb=" NE ARG B 85 " ideal model delta sigma weight residual 112.00 131.50 -19.50 2.20e+00 2.07e-01 7.86e+01 angle pdb=" CG ARG E 85 " pdb=" CD ARG E 85 " pdb=" NE ARG E 85 " ideal model delta sigma weight residual 112.00 131.46 -19.46 2.20e+00 2.07e-01 7.82e+01 angle pdb=" CD ARG E 85 " pdb=" NE ARG E 85 " pdb=" CZ ARG E 85 " ideal model delta sigma weight residual 124.40 132.31 -7.91 1.40e+00 5.10e-01 3.19e+01 angle pdb=" CD ARG B 85 " pdb=" NE ARG B 85 " pdb=" CZ ARG B 85 " ideal model delta sigma weight residual 124.40 132.25 -7.85 1.40e+00 5.10e-01 3.14e+01 angle pdb=" CB ARG E 85 " pdb=" CG ARG E 85 " pdb=" CD ARG E 85 " ideal model delta sigma weight residual 111.30 123.84 -12.54 2.30e+00 1.89e-01 2.97e+01 ... (remaining 19035 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.66: 8026 21.66 - 43.32: 426 43.32 - 64.98: 66 64.98 - 86.64: 32 86.64 - 108.30: 8 Dihedral angle restraints: 8558 sinusoidal: 3580 harmonic: 4978 Sorted by residual: dihedral pdb=" C ASP F 151 " pdb=" N ASP F 151 " pdb=" CA ASP F 151 " pdb=" CB ASP F 151 " ideal model delta harmonic sigma weight residual -122.60 -137.12 14.52 0 2.50e+00 1.60e-01 3.38e+01 dihedral pdb=" C ASP C 151 " pdb=" N ASP C 151 " pdb=" CA ASP C 151 " pdb=" CB ASP C 151 " ideal model delta harmonic sigma weight residual -122.60 -137.12 14.52 0 2.50e+00 1.60e-01 3.38e+01 dihedral pdb=" CG ARG B 85 " pdb=" CD ARG B 85 " pdb=" NE ARG B 85 " pdb=" CZ ARG B 85 " ideal model delta sinusoidal sigma weight residual -90.00 -9.21 -80.79 2 1.50e+01 4.44e-03 2.08e+01 ... (remaining 8555 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 1895 0.088 - 0.175: 262 0.175 - 0.263: 19 0.263 - 0.351: 4 0.351 - 0.438: 2 Chirality restraints: 2182 Sorted by residual: chirality pdb=" CA ASP C 151 " pdb=" N ASP C 151 " pdb=" C ASP C 151 " pdb=" CB ASP C 151 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.80e+00 chirality pdb=" CA ASP F 151 " pdb=" N ASP F 151 " pdb=" C ASP F 151 " pdb=" CB ASP F 151 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.79e+00 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN A 61 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.62e+00 ... (remaining 2179 not shown) Planarity restraints: 2440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 69 " 0.060 5.00e-02 4.00e+02 8.97e-02 1.29e+01 pdb=" N PRO B 70 " -0.155 5.00e-02 4.00e+02 pdb=" CA PRO B 70 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO B 70 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 69 " -0.060 5.00e-02 4.00e+02 8.95e-02 1.28e+01 pdb=" N PRO E 70 " 0.155 5.00e-02 4.00e+02 pdb=" CA PRO E 70 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO E 70 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 85 " 0.129 9.50e-02 1.11e+02 6.27e-02 9.55e+00 pdb=" NE ARG E 85 " 0.008 2.00e-02 2.50e+03 pdb=" CZ ARG E 85 " -0.049 2.00e-02 2.50e+03 pdb=" NH1 ARG E 85 " 0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG E 85 " 0.020 2.00e-02 2.50e+03 ... (remaining 2437 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 254 2.65 - 3.22: 12538 3.22 - 3.78: 20119 3.78 - 4.34: 26435 4.34 - 4.90: 42637 Nonbonded interactions: 101983 Sorted by model distance: nonbonded pdb=" OG SER D 261 " pdb=" OG SER F 247 " model vdw 2.093 3.040 nonbonded pdb=" OG SER A 261 " pdb=" OG SER C 247 " model vdw 2.100 3.040 nonbonded pdb=" NE2 GLN B 38 " pdb=" OE1 GLU B 104 " model vdw 2.135 3.120 nonbonded pdb=" NE2 GLN E 38 " pdb=" OE1 GLU E 104 " model vdw 2.136 3.120 nonbonded pdb=" OG1 THR A 347 " pdb=" OG1 THR A 377 " model vdw 2.150 3.040 ... (remaining 101978 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.07 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'I' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 0.580 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 34.650 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6576 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 13948 Z= 0.203 Angle : 1.211 19.503 19114 Z= 0.630 Chirality : 0.059 0.438 2182 Planarity : 0.007 0.090 2432 Dihedral : 14.568 108.305 5298 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 16.97 Ramachandran Plot: Outliers : 0.59 % Allowed : 5.52 % Favored : 93.89 % Rotamer: Outliers : 0.41 % Allowed : 2.39 % Favored : 97.20 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.19), residues: 1702 helix: 1.25 (0.29), residues: 250 sheet: -0.06 (0.20), residues: 558 loop : -1.42 (0.19), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP D 142 HIS 0.012 0.001 HIS E 86 PHE 0.039 0.003 PHE D 36 TYR 0.020 0.003 TYR A 344 ARG 0.047 0.001 ARG B 85 Details of bonding type rmsd link_NAG-ASN : bond 0.00927 ( 8) link_NAG-ASN : angle 3.18960 ( 24) link_BETA1-4 : bond 0.00723 ( 6) link_BETA1-4 : angle 3.51647 ( 18) hydrogen bonds : bond 0.25308 ( 520) hydrogen bonds : angle 8.79719 ( 1410) SS BOND : bond 0.00269 ( 16) SS BOND : angle 2.64312 ( 32) covalent geometry : bond 0.00445 (13918) covalent geometry : angle 1.19847 (19040) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 178 time to evaluate : 1.461 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.7698 (m) cc_final: 0.7137 (t) REVERT: A 220 LEU cc_start: 0.7337 (OUTLIER) cc_final: 0.7004 (mp) REVERT: B 109 GLN cc_start: 0.8246 (tm-30) cc_final: 0.7859 (tm-30) REVERT: C 157 ARG cc_start: 0.7161 (ptm-80) cc_final: 0.6855 (ttp-170) REVERT: C 282 TRP cc_start: 0.7501 (m100) cc_final: 0.6368 (m100) REVERT: D 35 TYR cc_start: 0.7123 (t80) cc_final: 0.6696 (t80) REVERT: D 57 TYR cc_start: 0.6498 (m-80) cc_final: 0.6284 (m-80) REVERT: D 220 LEU cc_start: 0.7213 (OUTLIER) cc_final: 0.6846 (mp) REVERT: F 157 ARG cc_start: 0.7134 (ptm-80) cc_final: 0.6855 (ttp-170) REVERT: F 202 LEU cc_start: 0.6647 (tp) cc_final: 0.6293 (tp) REVERT: F 282 TRP cc_start: 0.7522 (m100) cc_final: 0.6403 (m100) outliers start: 6 outliers final: 0 residues processed: 180 average time/residue: 0.2560 time to fit residues: 67.0000 Evaluate side-chains 120 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 118 time to evaluate : 1.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain D residue 220 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 5.9990 chunk 127 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 85 optimal weight: 0.0060 chunk 68 optimal weight: 9.9990 chunk 131 optimal weight: 1.9990 chunk 50 optimal weight: 0.2980 chunk 80 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 chunk 152 optimal weight: 0.8980 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN D 115 ASN F 229 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4671 r_free = 0.4671 target = 0.230162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.203176 restraints weight = 179609.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.205084 restraints weight = 109457.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.204556 restraints weight = 91612.956| |-----------------------------------------------------------------------------| r_work (final): 0.4115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 13948 Z= 0.165 Angle : 0.809 9.464 19114 Z= 0.396 Chirality : 0.048 0.295 2182 Planarity : 0.006 0.057 2432 Dihedral : 8.966 70.291 2160 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.94 % Favored : 96.94 % Rotamer: Outliers : 0.82 % Allowed : 7.65 % Favored : 91.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.20), residues: 1702 helix: 1.99 (0.30), residues: 252 sheet: 0.35 (0.20), residues: 546 loop : -0.38 (0.21), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 147 HIS 0.006 0.001 HIS E 161 PHE 0.016 0.002 PHE F 230 TYR 0.023 0.002 TYR C 103 ARG 0.008 0.001 ARG B 85 Details of bonding type rmsd link_NAG-ASN : bond 0.00443 ( 8) link_NAG-ASN : angle 1.68798 ( 24) link_BETA1-4 : bond 0.00659 ( 6) link_BETA1-4 : angle 2.82483 ( 18) hydrogen bonds : bond 0.05253 ( 520) hydrogen bonds : angle 6.11646 ( 1410) SS BOND : bond 0.00782 ( 16) SS BOND : angle 1.64429 ( 32) covalent geometry : bond 0.00369 (13918) covalent geometry : angle 0.80095 (19040) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 146 time to evaluate : 1.392 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 288 GLU cc_start: 0.6974 (mm-30) cc_final: 0.6687 (mm-30) outliers start: 12 outliers final: 4 residues processed: 156 average time/residue: 0.2223 time to fit residues: 52.4974 Evaluate side-chains 116 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 112 time to evaluate : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain F residue 151 ASP Chi-restraints excluded: chain F residue 230 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 5.9990 chunk 47 optimal weight: 0.0870 chunk 126 optimal weight: 5.9990 chunk 103 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 152 optimal weight: 10.0000 chunk 165 optimal weight: 0.7980 chunk 136 optimal weight: 0.3980 chunk 151 optimal weight: 0.7980 chunk 52 optimal weight: 0.3980 chunk 122 optimal weight: 0.8980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 GLN C 14 GLN F 14 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4673 r_free = 0.4673 target = 0.229703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.200006 restraints weight = 180817.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.204373 restraints weight = 106859.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.202139 restraints weight = 91942.628| |-----------------------------------------------------------------------------| r_work (final): 0.4122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 13948 Z= 0.139 Angle : 0.715 14.331 19114 Z= 0.346 Chirality : 0.046 0.301 2182 Planarity : 0.005 0.060 2432 Dihedral : 7.166 57.418 2156 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.82 % Favored : 97.06 % Rotamer: Outliers : 1.50 % Allowed : 10.38 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.20), residues: 1702 helix: 1.67 (0.31), residues: 262 sheet: 0.39 (0.20), residues: 556 loop : -0.16 (0.22), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 166 HIS 0.009 0.001 HIS C 229 PHE 0.018 0.001 PHE D 50 TYR 0.016 0.002 TYR A 344 ARG 0.006 0.001 ARG C 235 Details of bonding type rmsd link_NAG-ASN : bond 0.00365 ( 8) link_NAG-ASN : angle 1.57159 ( 24) link_BETA1-4 : bond 0.00691 ( 6) link_BETA1-4 : angle 2.87325 ( 18) hydrogen bonds : bond 0.04366 ( 520) hydrogen bonds : angle 5.48571 ( 1410) SS BOND : bond 0.01209 ( 16) SS BOND : angle 2.17962 ( 32) covalent geometry : bond 0.00307 (13918) covalent geometry : angle 0.70338 (19040) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 141 time to evaluate : 1.530 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 35 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7743 (tt) REVERT: B 89 TRP cc_start: 0.8569 (t60) cc_final: 0.8230 (t60) REVERT: C 95 VAL cc_start: 0.8147 (t) cc_final: 0.7875 (m) REVERT: D 280 MET cc_start: 0.6950 (ttt) cc_final: 0.6721 (ttt) REVERT: F 202 LEU cc_start: 0.6674 (tp) cc_final: 0.6431 (tp) outliers start: 22 outliers final: 13 residues processed: 158 average time/residue: 0.2145 time to fit residues: 52.9869 Evaluate side-chains 126 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 160 CYS Chi-restraints excluded: chain F residue 151 ASP Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 230 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 0.6980 chunk 114 optimal weight: 30.0000 chunk 79 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 102 optimal weight: 4.9990 chunk 153 optimal weight: 2.9990 chunk 162 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 145 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 GLN ** D 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.213743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.200018 restraints weight = 17396.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.185620 restraints weight = 36690.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.183239 restraints weight = 28233.021| |-----------------------------------------------------------------------------| r_work (final): 0.4159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13948 Z= 0.152 Angle : 0.702 12.565 19114 Z= 0.340 Chirality : 0.046 0.307 2182 Planarity : 0.005 0.062 2432 Dihedral : 6.429 57.751 2156 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.32 % Allowed : 12.64 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.20), residues: 1702 helix: 1.69 (0.32), residues: 252 sheet: 0.31 (0.20), residues: 560 loop : 0.08 (0.22), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 166 HIS 0.015 0.001 HIS F 229 PHE 0.014 0.002 PHE C 230 TYR 0.016 0.002 TYR C 103 ARG 0.004 0.000 ARG B 118 Details of bonding type rmsd link_NAG-ASN : bond 0.00315 ( 8) link_NAG-ASN : angle 1.62992 ( 24) link_BETA1-4 : bond 0.00524 ( 6) link_BETA1-4 : angle 2.78221 ( 18) hydrogen bonds : bond 0.03973 ( 520) hydrogen bonds : angle 5.24033 ( 1410) SS BOND : bond 0.00427 ( 16) SS BOND : angle 2.17912 ( 32) covalent geometry : bond 0.00349 (13918) covalent geometry : angle 0.68984 (19040) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 122 time to evaluate : 1.386 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 35 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7369 (tt) REVERT: B 89 TRP cc_start: 0.8678 (t60) cc_final: 0.8369 (t60) REVERT: C 164 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.7444 (tp30) REVERT: F 164 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.7847 (tp30) outliers start: 34 outliers final: 17 residues processed: 150 average time/residue: 0.1940 time to fit residues: 47.4987 Evaluate side-chains 132 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 160 CYS Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain F residue 151 ASP Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain F residue 183 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 0.8980 chunk 137 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 55 optimal weight: 9.9990 chunk 50 optimal weight: 0.0970 chunk 102 optimal weight: 6.9990 chunk 41 optimal weight: 0.9980 chunk 164 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 GLN A 82 ASN ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 GLN ** C 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 ASN ** D 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.209345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.196402 restraints weight = 17626.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.183669 restraints weight = 34184.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.177188 restraints weight = 29663.537| |-----------------------------------------------------------------------------| r_work (final): 0.4115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 13948 Z= 0.160 Angle : 0.697 16.449 19114 Z= 0.340 Chirality : 0.046 0.322 2182 Planarity : 0.005 0.062 2432 Dihedral : 6.086 57.540 2156 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.46 % Allowed : 13.73 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.20), residues: 1702 helix: 1.48 (0.32), residues: 252 sheet: 0.29 (0.20), residues: 544 loop : 0.07 (0.22), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 166 HIS 0.015 0.001 HIS C 229 PHE 0.025 0.002 PHE F 230 TYR 0.017 0.002 TYR F 103 ARG 0.003 0.000 ARG C 93 Details of bonding type rmsd link_NAG-ASN : bond 0.00306 ( 8) link_NAG-ASN : angle 1.71000 ( 24) link_BETA1-4 : bond 0.00514 ( 6) link_BETA1-4 : angle 2.60355 ( 18) hydrogen bonds : bond 0.03780 ( 520) hydrogen bonds : angle 5.07660 ( 1410) SS BOND : bond 0.00824 ( 16) SS BOND : angle 2.33552 ( 32) covalent geometry : bond 0.00369 (13918) covalent geometry : angle 0.68434 (19040) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 126 time to evaluate : 1.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 GLN cc_start: 0.8078 (OUTLIER) cc_final: 0.7737 (mt0) REVERT: A 222 TRP cc_start: 0.8312 (p90) cc_final: 0.8081 (p90) REVERT: A 287 TYR cc_start: 0.5027 (m-10) cc_final: 0.4729 (m-10) REVERT: C 282 TRP cc_start: 0.7682 (m100) cc_final: 0.6859 (m100) REVERT: D 17 GLN cc_start: 0.8108 (mp10) cc_final: 0.7832 (mt0) REVERT: D 287 TYR cc_start: 0.5253 (m-10) cc_final: 0.4977 (m-10) outliers start: 36 outliers final: 20 residues processed: 153 average time/residue: 0.1942 time to fit residues: 48.6025 Evaluate side-chains 131 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLN Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain D residue 4 ASP Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 160 CYS Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain F residue 183 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 46 optimal weight: 1.9990 chunk 157 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 68 optimal weight: 9.9990 chunk 9 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 113 optimal weight: 0.7980 chunk 35 optimal weight: 8.9990 chunk 117 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 GLN ** C 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.207560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.194636 restraints weight = 17510.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.184289 restraints weight = 34356.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.177672 restraints weight = 25568.495| |-----------------------------------------------------------------------------| r_work (final): 0.4121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 13948 Z= 0.152 Angle : 0.692 16.697 19114 Z= 0.337 Chirality : 0.045 0.317 2182 Planarity : 0.005 0.063 2432 Dihedral : 6.032 57.479 2156 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.53 % Allowed : 14.55 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.21), residues: 1702 helix: 1.47 (0.32), residues: 252 sheet: 0.28 (0.21), residues: 534 loop : -0.01 (0.22), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 166 HIS 0.010 0.001 HIS C 229 PHE 0.031 0.002 PHE C 230 TYR 0.025 0.002 TYR F 103 ARG 0.003 0.000 ARG E 118 Details of bonding type rmsd link_NAG-ASN : bond 0.00295 ( 8) link_NAG-ASN : angle 1.77394 ( 24) link_BETA1-4 : bond 0.00450 ( 6) link_BETA1-4 : angle 2.54126 ( 18) hydrogen bonds : bond 0.03649 ( 520) hydrogen bonds : angle 4.94417 ( 1410) SS BOND : bond 0.00679 ( 16) SS BOND : angle 2.47221 ( 32) covalent geometry : bond 0.00350 (13918) covalent geometry : angle 0.67816 (19040) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 124 time to evaluate : 1.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 GLN cc_start: 0.8145 (mp10) cc_final: 0.7932 (mt0) REVERT: A 280 MET cc_start: 0.6739 (ttt) cc_final: 0.6486 (ttt) REVERT: A 287 TYR cc_start: 0.5260 (m-10) cc_final: 0.5033 (m-10) REVERT: C 164 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.7933 (tp30) REVERT: D 17 GLN cc_start: 0.8096 (mp10) cc_final: 0.7875 (mt0) REVERT: D 287 TYR cc_start: 0.5060 (m-10) cc_final: 0.4782 (m-10) REVERT: E 38 GLN cc_start: 0.8716 (OUTLIER) cc_final: 0.8461 (tt0) REVERT: F 164 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.7942 (tp30) outliers start: 37 outliers final: 23 residues processed: 155 average time/residue: 0.1885 time to fit residues: 47.3885 Evaluate side-chains 138 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 112 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain D residue 4 ASP Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 160 CYS Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 38 GLN Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain F residue 183 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 104 optimal weight: 7.9990 chunk 31 optimal weight: 7.9990 chunk 105 optimal weight: 0.7980 chunk 126 optimal weight: 5.9990 chunk 107 optimal weight: 0.4980 chunk 150 optimal weight: 8.9990 chunk 143 optimal weight: 2.9990 chunk 118 optimal weight: 7.9990 chunk 112 optimal weight: 0.4980 chunk 84 optimal weight: 0.9980 chunk 120 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 161 HIS C 73 GLN C 229 HIS ** D 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 161 HIS F 73 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.210596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.196108 restraints weight = 17496.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.182212 restraints weight = 36500.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.178286 restraints weight = 28830.727| |-----------------------------------------------------------------------------| r_work (final): 0.4107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13948 Z= 0.136 Angle : 0.681 16.550 19114 Z= 0.332 Chirality : 0.045 0.313 2182 Planarity : 0.005 0.061 2432 Dihedral : 5.938 57.394 2156 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.32 % Allowed : 15.51 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.21), residues: 1702 helix: 1.57 (0.32), residues: 252 sheet: 0.26 (0.21), residues: 526 loop : -0.02 (0.22), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 166 HIS 0.010 0.001 HIS F 229 PHE 0.017 0.002 PHE C 230 TYR 0.024 0.001 TYR C 103 ARG 0.003 0.000 ARG F 274 Details of bonding type rmsd link_NAG-ASN : bond 0.00282 ( 8) link_NAG-ASN : angle 1.73854 ( 24) link_BETA1-4 : bond 0.00476 ( 6) link_BETA1-4 : angle 2.50629 ( 18) hydrogen bonds : bond 0.03514 ( 520) hydrogen bonds : angle 4.87293 ( 1410) SS BOND : bond 0.00789 ( 16) SS BOND : angle 2.63501 ( 32) covalent geometry : bond 0.00310 (13918) covalent geometry : angle 0.66639 (19040) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 121 time to evaluate : 1.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 HIS cc_start: 0.7689 (p-80) cc_final: 0.7290 (p-80) REVERT: C 164 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.7947 (tp30) REVERT: D 280 MET cc_start: 0.6371 (ttt) cc_final: 0.6101 (ttt) REVERT: E 38 GLN cc_start: 0.8651 (OUTLIER) cc_final: 0.8439 (tt0) REVERT: F 164 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.7819 (tp30) outliers start: 34 outliers final: 30 residues processed: 150 average time/residue: 0.1948 time to fit residues: 47.2386 Evaluate side-chains 138 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 105 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 230 PHE Chi-restraints excluded: chain D residue 4 ASP Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 86 PHE Chi-restraints excluded: chain D residue 123 GLU Chi-restraints excluded: chain D residue 160 CYS Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 38 GLN Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 151 ASP Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 207 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 140 optimal weight: 20.0000 chunk 35 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 chunk 150 optimal weight: 0.0870 chunk 157 optimal weight: 0.4980 chunk 54 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 68 optimal weight: 5.9990 chunk 129 optimal weight: 1.9990 overall best weight: 0.7164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.208238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.195157 restraints weight = 17774.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.183032 restraints weight = 34889.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.179989 restraints weight = 28454.849| |-----------------------------------------------------------------------------| r_work (final): 0.4122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13948 Z= 0.135 Angle : 0.689 18.253 19114 Z= 0.334 Chirality : 0.045 0.313 2182 Planarity : 0.005 0.079 2432 Dihedral : 5.849 57.556 2156 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.87 % Allowed : 15.85 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.21), residues: 1702 helix: 1.58 (0.33), residues: 252 sheet: 0.25 (0.22), residues: 540 loop : -0.02 (0.22), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 222 HIS 0.009 0.001 HIS E 49 PHE 0.011 0.001 PHE F 230 TYR 0.024 0.001 TYR C 103 ARG 0.003 0.000 ARG E 118 Details of bonding type rmsd link_NAG-ASN : bond 0.00271 ( 8) link_NAG-ASN : angle 1.78033 ( 24) link_BETA1-4 : bond 0.00514 ( 6) link_BETA1-4 : angle 2.48243 ( 18) hydrogen bonds : bond 0.03432 ( 520) hydrogen bonds : angle 4.81310 ( 1410) SS BOND : bond 0.00578 ( 16) SS BOND : angle 2.63627 ( 32) covalent geometry : bond 0.00311 (13918) covalent geometry : angle 0.67439 (19040) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 122 time to evaluate : 1.421 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 MET cc_start: 0.5930 (tmm) cc_final: 0.5676 (tmm) REVERT: A 185 VAL cc_start: 0.9063 (OUTLIER) cc_final: 0.8857 (t) REVERT: A 232 ILE cc_start: 0.8821 (OUTLIER) cc_final: 0.8584 (mm) REVERT: B 49 HIS cc_start: 0.7719 (p-80) cc_final: 0.7369 (p-80) REVERT: C 164 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.7991 (tp30) REVERT: D 185 VAL cc_start: 0.9059 (OUTLIER) cc_final: 0.8831 (t) REVERT: F 164 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.7917 (tp30) outliers start: 42 outliers final: 29 residues processed: 156 average time/residue: 0.1857 time to fit residues: 47.1396 Evaluate side-chains 145 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 111 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 230 PHE Chi-restraints excluded: chain D residue 4 ASP Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 160 CYS Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 207 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 51 optimal weight: 7.9990 chunk 107 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 chunk 114 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 52 optimal weight: 0.0670 chunk 152 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.209846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.197623 restraints weight = 17570.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.182722 restraints weight = 31708.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.177558 restraints weight = 32212.080| |-----------------------------------------------------------------------------| r_work (final): 0.4079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.4101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13948 Z= 0.126 Angle : 0.696 18.384 19114 Z= 0.337 Chirality : 0.045 0.304 2182 Planarity : 0.005 0.064 2432 Dihedral : 5.794 57.363 2156 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.39 % Allowed : 17.14 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.21), residues: 1702 helix: 1.67 (0.33), residues: 252 sheet: 0.29 (0.21), residues: 540 loop : -0.04 (0.22), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 222 HIS 0.014 0.001 HIS F 229 PHE 0.021 0.001 PHE F 230 TYR 0.032 0.001 TYR F 103 ARG 0.008 0.000 ARG F 235 Details of bonding type rmsd link_NAG-ASN : bond 0.00293 ( 8) link_NAG-ASN : angle 1.76169 ( 24) link_BETA1-4 : bond 0.00457 ( 6) link_BETA1-4 : angle 2.45156 ( 18) hydrogen bonds : bond 0.03347 ( 520) hydrogen bonds : angle 4.78617 ( 1410) SS BOND : bond 0.00429 ( 16) SS BOND : angle 2.83962 ( 32) covalent geometry : bond 0.00287 (13918) covalent geometry : angle 0.68076 (19040) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 116 time to evaluate : 1.457 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 49 HIS cc_start: 0.7744 (p-80) cc_final: 0.7468 (p-80) REVERT: C 164 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.7592 (mm-30) REVERT: F 164 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.7746 (mm-30) outliers start: 35 outliers final: 27 residues processed: 144 average time/residue: 0.1935 time to fit residues: 45.2775 Evaluate side-chains 136 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 107 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 230 PHE Chi-restraints excluded: chain D residue 4 ASP Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 86 PHE Chi-restraints excluded: chain D residue 160 CYS Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 207 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 22 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 153 optimal weight: 0.7980 chunk 59 optimal weight: 20.0000 chunk 68 optimal weight: 2.9990 chunk 43 optimal weight: 0.0980 chunk 86 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 159 optimal weight: 3.9990 chunk 149 optimal weight: 0.5980 chunk 60 optimal weight: 8.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.217291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.188101 restraints weight = 181839.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.190537 restraints weight = 111136.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.189614 restraints weight = 94158.234| |-----------------------------------------------------------------------------| r_work (final): 0.4004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.4213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13948 Z= 0.135 Angle : 0.706 17.840 19114 Z= 0.342 Chirality : 0.045 0.306 2182 Planarity : 0.005 0.067 2432 Dihedral : 5.787 57.521 2156 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.91 % Allowed : 17.90 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.21), residues: 1702 helix: 1.66 (0.33), residues: 252 sheet: 0.27 (0.21), residues: 540 loop : -0.05 (0.22), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP F 282 HIS 0.014 0.001 HIS C 229 PHE 0.020 0.001 PHE F 230 TYR 0.026 0.001 TYR F 103 ARG 0.004 0.000 ARG F 274 Details of bonding type rmsd link_NAG-ASN : bond 0.00284 ( 8) link_NAG-ASN : angle 1.78599 ( 24) link_BETA1-4 : bond 0.00514 ( 6) link_BETA1-4 : angle 2.43654 ( 18) hydrogen bonds : bond 0.03370 ( 520) hydrogen bonds : angle 4.81506 ( 1410) SS BOND : bond 0.00610 ( 16) SS BOND : angle 2.86404 ( 32) covalent geometry : bond 0.00313 (13918) covalent geometry : angle 0.69064 (19040) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 118 time to evaluate : 1.487 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 MET cc_start: 0.6348 (tmm) cc_final: 0.6102 (tmm) REVERT: B 49 HIS cc_start: 0.7887 (p-80) cc_final: 0.7604 (p-80) REVERT: C 164 GLU cc_start: 0.8835 (OUTLIER) cc_final: 0.7727 (mm-30) REVERT: F 164 GLU cc_start: 0.8906 (OUTLIER) cc_final: 0.7980 (mm-30) outliers start: 28 outliers final: 24 residues processed: 140 average time/residue: 0.1933 time to fit residues: 43.7295 Evaluate side-chains 138 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 112 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain D residue 4 ASP Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 160 CYS Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 207 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 96 optimal weight: 6.9990 chunk 83 optimal weight: 4.9990 chunk 155 optimal weight: 0.7980 chunk 135 optimal weight: 8.9990 chunk 153 optimal weight: 0.0770 chunk 39 optimal weight: 0.7980 chunk 146 optimal weight: 7.9990 chunk 82 optimal weight: 3.9990 chunk 139 optimal weight: 7.9990 chunk 140 optimal weight: 6.9990 chunk 85 optimal weight: 0.0570 overall best weight: 1.1458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.213039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.182865 restraints weight = 183230.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.185572 restraints weight = 112376.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.183733 restraints weight = 96908.789| |-----------------------------------------------------------------------------| r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.4420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 13948 Z= 0.174 Angle : 0.733 16.648 19114 Z= 0.357 Chirality : 0.047 0.321 2182 Planarity : 0.005 0.065 2432 Dihedral : 5.874 58.163 2156 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.84 % Allowed : 18.10 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.21), residues: 1702 helix: 1.42 (0.32), residues: 252 sheet: 0.15 (0.21), residues: 544 loop : -0.08 (0.23), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 166 HIS 0.023 0.002 HIS C 229 PHE 0.029 0.002 PHE C 230 TYR 0.032 0.002 TYR F 103 ARG 0.004 0.000 ARG C 274 Details of bonding type rmsd link_NAG-ASN : bond 0.00242 ( 8) link_NAG-ASN : angle 1.87834 ( 24) link_BETA1-4 : bond 0.00470 ( 6) link_BETA1-4 : angle 2.50770 ( 18) hydrogen bonds : bond 0.03615 ( 520) hydrogen bonds : angle 4.88945 ( 1410) SS BOND : bond 0.00932 ( 16) SS BOND : angle 2.98795 ( 32) covalent geometry : bond 0.00409 (13918) covalent geometry : angle 0.71685 (19040) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3820.38 seconds wall clock time: 68 minutes 4.54 seconds (4084.54 seconds total)